Library Guides: Bioinformatics: All resources

Selected bioinformatics resources

This page lists all bioinformatics resources included in this guide in alphabetical order. Browse the list or search within the page using Crtl+F.

BDGP (Berkeley Drosophila Genome Project)
A consortium working to sequence the euchromatic genome of Drosophila melanogaster and to generate and maintain biological annotations of this sequence.

BioCyc This link opens in a new window
Genomes and predicted metabolic pathways for thousands of organisms, together with a suite of software tools for analysis and visualization. Login to a free personal account is required after 10 searches.
Pathway/Genome Databases (PGDBs) are generated by software that predict the metabolic pathways of completely sequenced organisms, predict which genes code for missing enzymes in metabolic pathways, and predict operons. BioCyc also integrates information from other bioinformatics databases, such as protein feature and Gene Ontology information from UniProt. The BioCyc website provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions.

Broad Institute
Freely available data, software and tools for genomic analysis (archived link page; some links may no longer work).
California Biobank Program
The California Biobank Program (CBP) represents the combined biospecimen and data resources of two California Department of Public Health (CDPH) screening and monitoring programs, the California Birth Defects Monitoring Program (CBDMP) and the California Genetic Disease Screening Program (GDSP). GDSP administers both the Newborn Screening Program (NBS) and the Prenatal Screening Program (PNS).
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The CBP has been mandated to make specimens and data available to researchers to identify risk factors for children's and women's diseases, develop and evaluate screening tests, develop and evaluate screening strategies, and develop and evaluate treatments.
DDBJ (DNA Data Bank of Japan)
A public database of annotated nucleotide sequences. Includes the Japanese Genotype-phenotype Archive (JGA), personal genotype and phenotype data from individuals who have signed consent agreements authorizing data release only for specific research uses.
DGRC (Drosophila Genomics Resource Center)
DNA clones, vectors and cell lines for Drosophila species.
EcoCyc
A database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.
EcoSal Plus
A review journal covering Escherichia coli (E. coli), Salmonella, and other members of the Enterobacteriaceae family and their use as model microbes.
ELIXIR
ELIXIR (The European Life-Science Infrastructure for Biological Information Resources) is an intergovernmental organization that provides a single integrated infrastructure for bioinformatics data, software tools, and training materials.
EMBL-EBI (European Bioinformatics Institute)
A collection of freely available tools and data resources including AlphaFold (protein structures), BioModels (computational models), ChEMBL (bioactive compounds), Ensembl (genome browser), Expression Atlas (gene expression), GWAS Catalog (genome-wide association studies), Protein Data Bank (3D structures), and UniProt (protein sequences).
ExPASy
Portal of the SIB Swiss Institute of Bioinformatics to databases and software tools in proteomics, genomics, phylogeny, systems biology, evolution, population genetics, and transcriptomics. Formerly the Expert Protein Analysis System.
GDC (Genomic Data Commons of the National Cancer Institute)
NCI-generated data from cancer genomic datasets, including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Therapies (TARGET), supporting the elucidation of the molecular basis of cancer.
Hymenoptera Genome Database (HGD)
Genome sequence data for insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD integrates with the data mining tool HymenopteraMine.
JGI (Joint Genome Institute)
Tools for the analysis and functional characterization of publicly available genomes of plants, fungi, and microbes, as well as environmental metagenomes.
KEGG (Kyoto Encyclopedia of Genes and Genomes)
Resource for the integration and interpretation of large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
MaizeGDB (Maize Genetics and Genomics Database)
Sequence and analysis resources on the crop plant and model organism Zea mays.
MetaCyc
A curated database of experimentally elucidated metabolic pathways from thousands of different organisms from all domains of life.
MGI (Mouse Genome Informatics)
Genetic, genomic, and biological data to facilitate the study of the laboratory mouse as a model organism for human health and disease.
miRBase
A database of published miRNA sequences and annotations for hundreds of different species.
NCBI (National Center for Biotechnology Information)
A federally-supported collection of more than 40 databases and analysis tools for research in molecular biology, including Assembly, Basic Local Alignment Search Tool (BLAST), BioProject, BioSample, Gene, Gene Expression Omnibus (GEO), Genome, Nucleotide, Protein, Structure, and the Sequence Read Archive (SRA).
NCBI Guide
OBRC (Online Bioinformatics Resources Collection)
Descriptions and links for hundreds of bioinformatics databases and software tools.
PomBase
Structural and functional annotation, literature curation and large-scale data sets for the fission yeast Schizosaccharomyces pombe.

Proteome This link opens in a new window
Protein information for species including human, mouse, rat, yeast, worm, and plant, including links to relevant scientific literature. Human entries include associated disease information.
PubMed This link opens in a new window
Citations and abstracts in the fields of biomedicine and health, as well as portions of the life sciences, behavioral sciences, chemical sciences, and bioengineering.

PubMed includes MEDLINE, PubMed Central (PMC), other biomedical and life science journals, and the NCBI Bookshelf. PubMed also provides links to other NCBI molecular biology resources, including nucleotide sequences, protein sequences, 3-D protein structure data, population study data sets, and assemblies of complete genomes in an integrated system.
Note: The link above goes to a specially configured version of PubMed for UC Berkeley users that will display the Get It at UC button for full text article access. To use the free public version, please click here.
Repbase This link opens in a new window
A database of prototypic sequences representing repetitive DNA from different eukaryotic species, together with analytical software.
Used in genome sequencing projects such as RepeatMasker or CENSOR as a reference collection for masking and annotation of repetitive DNA.

SGD (Saccharomyces Genome Database)
Integrated biological resources for the budding yeast Saccharomyces cerevisiae along with search and analysis tools.
TAIR (The Arabidopsis Information Resource)
Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.
UCSC Genome Browser
Vertebrate and model organism genome assemblies and annotations, together with a suite of tools for data viewing, analysis and download.
UCSC Xena
Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables. The next generation of the UCSC Cancer Genomics Browser.
VectorBase
Provides genomic, phenotypic and population-centric data for invertebrate vectors of human pathogens. Sponsored by NIAID-BRC (National Institute of Allergy and Infectious Diseases Bioinformatics Resource Center).
WormBase
A resource on the genetics, genomics and biology of C. elegans and related nematodes
XenBase
Genomic, expression and functional data for the model organisms Xenopus laevis and X. tropicalis.
ZFIN (Zebrafish Information Network)
The zebrafish model organism database, including reference information on zebrafish genetics, genomics and development.

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Elliott Smith

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Contact:

Bioscience, Natural Resources &
Public Health Library
epsmith@berkeley.edu

Subjects: Biological Sciences, Biology, Comparative Biochemistry, Integrative Biology, Molecular and Cell Biology, Neuroscience

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Bioinformatics: All resources

Selected bioinformatics resources

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